MolNFT v1 · #134991 · protein
Complex between human CD27 and Fab fragments of antibodies M2177 and M2191
5TLJ · M2177 light chain: “Complex between human CD27 and Fab fragments of antibodies M2177 and M2191”. X-ray diffraction, 1 ligand (NAG), 13 pockets (best druggability 0.70). MolNFT v1 #134991 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5TLJ
- Type
- protein
- Length
- 1,808 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M2177 light chain; M2177 heavy chain; M2191 light chain; M2191 heavy chain; CD27 antigen
- UniProt
- P26842
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | M2177 light chain | protein | 215 | 5% helix, 50% strand | — |
| B, F | M2177 heavy chain | protein | 220 | 3% helix, 49% strand | — |
| C, G | M2191 light chain | protein | 215 | 4% helix, 49% strand | — |
| D, H | M2191 heavy chain | protein | 217 | 3% helix, 51% strand | — |
| X | CD27 antigen | protein | 74 | 0% helix, 24% strand | P26842 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains X, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.70 | 0.74 | 109 | empty |
| 2 | 735 | 0.66 | 0.75 | 69 | empty |
| 3 | 621 | 0.65 | 0.75 | 59 | empty |
| 4 | 618 | 0.64 | 0.75 | 63 | empty |
| 5 | 324 | 0.61 | 0.78 | 33 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1991 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1971 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1929 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1907 Ų buried · 11 hydrogen bonds · protein-protein
- D–X · 509 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 2 modified, 1 glycan (disulfide, cyclization, N-glycosylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P26842
- Elsewhere: RCSB PDB 5TLJ · PDBe 5TLJ · UniProt P26842
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